Josh Lamstein
Senior Bioinformatics Engineer
San Francisco, California, United States
Summary
👤
Senior🎓
Top SchoolJosh Lamstein is a Senior Bioinformatics Engineer in San Francisco with eight years of experience applying deep learning and physics-informed thinking to neuroscience and live-cell imaging. He builds production-grade image analysis pipelines and closed-loop ML microscopes, integrating tools like Nextflow, Postgres, Kafka, Docker, and distributed compute to move research from lab to scalable systems. His background in physics and hands-on optics work informs novel approaches to imaging problems—he's found subtle biological signals with XAI and led development of graph- and Siamese-CNN-based tracking and classification models. Comfortable across research and engineering, he has hired and mentored engineers and interns while consolidating robotic microscope codebases across multiple instruments. Curious about how systems shape outcomes, he blends rigorous experimentation with pragmatic software practices to deliver reproducible, deployable bioinformatics solutions.
8 years of coding experience
2 years of employment as a software developer
Master of Science (M.S.) Physics, Master of Science (M.S.) Physics at San Francisco State UniversityBachelor of Arts (B.A.) English Language and Literature/Letters, Bachelor of Arts (B.A.) English Language and Literature/Letters at Oberlin College
English, Spanish
Github Skills (30)
python10
machine-learning10
ml10
deep-learning10
tensorflow10
deep-neural-networks10
neural-network10
bioinformatics9
nextflow8
reproducible-research8
singularity8
slurm8
reproducible-science8
dataflow7
dsl7
Programming languages (5)
Github contributions (5)
finkbeiner-lab/datastudy
Nov 2023 - Nov 2025
Analysis Pipeline Using Nextflow
Contributions:1 review, 1 PR, 42 pushes in 2 years
finkbeiner-lab/GEDI-ORDER
Aug 2020 - May 2023
Use cell morphology to determine if the cell is live or dead with a CNN.
Contributions:1 release, 2 PRs, 85 pushes in 2 years 9 months
morphologydeep-learningcell-morphologydeterminecnn
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